[English] 日本語
Yorodumi
- PDB-1c4q: MUTATED SHIGA-LIKE TOXIN B SUBUNIT (F30A/W34A) COMPLEXED WITH REC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c4q
TitleMUTATED SHIGA-LIKE TOXIN B SUBUNIT (F30A/W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE
ComponentsPROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)
KeywordsTOXIN / RECEPTOR BINDING / PROTEIN-CARBOHYDRATE RECOGNITION / OB-FOLD
Function / homology
Function and homology information


symbiont-mediated modulation of host virulence / hemolysis by symbiont of host erythrocytes / toxin activity / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #70 / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Shiga-like toxin 1 subunit B / Shiga-like toxin 1 subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsLing, H. / Brunton, J.L. / Read, R.J.
Citation
Journal: To be Published
Title: Identification of the Primary Receptor Binding Site of Shiga-Like Toxin B Subunits: Structures of Mutated Shiga-Like Toxin I B-Pentamer with and without Bound Carbohydrate
Authors: Ling, H. / Bast, D. / Brunton, J.L. / Read, R.J.
#1: Journal: Biochemistry / Year: 1998
Title: Structure of the Shiga-Like Toxin I B-Pentamer Complexed with an Analogue of its Receptor Gb3
Authors: Ling, H. / La Boodhoo, J. / Hazes, B. / Cummings, M.D. / Armstrong, G.D. / Brunton, J.L. / Read, R.J.
History
DepositionAug 31, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)
B: PROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)
C: PROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)
D: PROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)
E: PROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,05910
Polymers37,5375
Non-polymers2,5225
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint10 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.269, 44.165, 54.007
Angle α, β, γ (deg.)106.24, 106.69, 98.87
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.339709, -0.926657, -0.160949), (0.931875, 0.308455, 0.190956), (-0.127306, -0.214854, 0.968314)29.116, -39.9257, 4.8519
2given(-0.663922, -0.59307, -0.455496), (0.615463, -0.779338, 0.117636), (-0.424751, -0.20224, 0.882432)73.4746, -26.8361, 18.2715
3given(-0.643159, 0.561526, -0.520611), (-0.582412, -0.800127, -0.143503), (-0.497135, 0.210914, 0.841648)72.8158, 25.0657, 20.7311
4given(0.329328, 0.936505, -0.120421), (-0.930738, 0.300504, -0.208384), (-0.158966, 0.180707, 0.970605)28.1841, 40.248, 7.868

-
Components

#1: Protein
PROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)


Mass: 7507.405 Da / Num. of mol.: 5 / Fragment: RECEPTOR-BINDING DOMAIN / Mutation: F30A, W34A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P08027, UniProt: P69179*PLUS
#2: Polysaccharide
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-4DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1a_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growpH: 7.5 / Details: pH 7.5

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1998
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.52→38.7 Å / Num. obs: 54074 / % possible obs: 96.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056
Reflection shellHighest resolution: 1.52 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.287 / Rsym value: 0.287 / % possible all: 82.7

-
Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
CNS0.3Drefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BOS

1bos


Resolution: 1.52→38.7 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1164 2.1 %THIN SHELLS
Rwork0.17 ---
obs0.17 54074 96.7 %-
Solvent computationBsol: 30.5 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.034 Å20.906 Å23.008 Å2
2---1.173 Å22.035 Å2
3---0.139 Å2
Refinement stepCycle: LAST / Resolution: 1.52→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 170 389 3232
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.8321.5
X-RAY DIFFRACTIONc_mcangle_it1.3452
X-RAY DIFFRACTIONc_scbond_it1.3062
X-RAY DIFFRACTIONc_scangle_it2.0522.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 1.52→1.54 Å / Total num. of bins used: 23
RfactorNum. reflection% reflection
Rfree0.319 241 1.3 %
Rwork0.301 1771 -
obs--82.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH3.CHO
X-RAY DIFFRACTION3PARAM3.CHOTOPH19.SOL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more